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The R,R-2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]-1,4-butandiol lignan secoisolariciresinol (1) is a constituent of Gymnosperms used in the treatment of benign prostatic hyperplasya. The results of crystallographic and ab initio theoretical studies are reported and discussed. In the crystal, the molecule of (1) assumes a clustered conformation, characterized by the facing of the two phenyl rings. This geometry is stabilized by the formation of a network of hydrogen bonds. Theoretical calculations indicate that: i) the intramolecular hydrogen bond O1−H1⋅⋅⋅O1' is the major factor dictating the facing of the two phenyl groups, while intermolecular hydrogen bonds and crystal packing have smaller effects; ii) the 1−4O⋅⋅⋅O non-bonded interactions in the vanillyl groups are important in determining the most stable conformation; iii) calculations with two explicit water molecules in the model give a good simulation of the local effects of a water solvent and indicate that (1) probably assumes a clustered conformation also in polar solvents.